diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index fd57ae55..3ed0cefa 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -7,7 +7,7 @@ on:
types: [run-all-tool-tests-command]
env:
GALAXY_FORK: galaxyproject
- GALAXY_BRANCH: release_23.2
+ GALAXY_BRANCH: release_24.0
MAX_CHUNKS: 40
jobs:
setup:
@@ -27,7 +27,7 @@ jobs:
steps:
- name: Add reaction
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
- uses: peter-evans/create-or-update-comment@v2
+ uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -43,11 +43,11 @@ jobs:
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -56,7 +56,7 @@ jobs:
# are not available as wheels, pip will build a wheel for them, which can be cached.
- name: Install wheel
run: pip install wheel
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -84,14 +84,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -104,7 +104,7 @@ jobs:
repository-list: ${{ needs.setup.outputs.repository-list }}
tool-list: ${{ needs.setup.outputs.tool-list }}
additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Tool linting output'
@@ -133,20 +133,20 @@ jobs:
steps:
# checkout the repository
# and use it as the current working directory
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
- uses: SimenB/github-actions-cpu-cores@v1
+ uses: SimenB/github-actions-cpu-cores@v2
id: cpu-cores
- name: Clean dotnet folder for space
run: rm -Rf /usr/share/dotnet
@@ -163,7 +163,7 @@ jobs:
galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
# Limit each test to 15 minutes
test_timeout: 900
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
@@ -182,14 +182,14 @@ jobs:
# This job runs on Linux
runs-on: ubuntu-latest
steps:
- - uses: actions/download-artifact@v3
+ - uses: actions/download-artifact@v4
with:
path: artifacts
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -200,7 +200,7 @@ jobs:
with:
mode: combine
html-report: true
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
with:
name: 'All tool test results'
path: upload
@@ -211,7 +211,7 @@ jobs:
- name: Create comment
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
- uses: peter-evans/create-or-update-comment@v2
+ uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 00d355cd..8591087f 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -2,7 +2,6 @@ name: Galaxy Tool Linting and Tests for push and PR
on:
pull_request:
paths-ignore:
- - '.github/**'
- 'deprecated/**'
- 'docs/**'
- '*'
@@ -11,13 +10,12 @@ on:
- main
- master
paths-ignore:
- - '.github/**'
- 'deprecated/**'
- 'docs/**'
- '*'
env:
GALAXY_FORK: galaxyproject
- GALAXY_BRANCH: release_23.2
+ GALAXY_BRANCH: release_24.0
MAX_CHUNKS: 4
MAX_FILE_SIZE: 1M
concurrency:
@@ -59,17 +57,17 @@ jobs:
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
- name: Cache .planemo
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-planemo
with:
path: ~/.planemo
@@ -80,7 +78,7 @@ jobs:
run: pip install wheel
- name: Install flake8
run: pip install flake8 flake8-import-order
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -113,14 +111,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -142,7 +140,7 @@ jobs:
fail-level: ${{ env.FAIL_LEVEL }}
repository-list: ${{ needs.setup.outputs.repository-list }}
tool-list: ${{ needs.setup.outputs.tool-list }}
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Tool linting output'
@@ -159,14 +157,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -175,7 +173,7 @@ jobs:
run: pip install flake8 flake8-import-order
- name: Flake8
run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Python linting output'
@@ -184,21 +182,21 @@ jobs:
lintr:
name: Lint R scripts
needs: setup
- if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
+ if: ${{ needs.setup.outputs.repository-list != '' }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-20.04]
r-version: ['release']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r-version }}
- name: Cache R packages
- uses: actions/cache@v3
+ uses: actions/cache@v4
with:
path: ${{ env.R_LIBS_USER }}
key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
@@ -214,7 +212,7 @@ jobs:
echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
git status
git diff --exit-code | tee rlint_report.txt
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'R linting output'
@@ -226,7 +224,7 @@ jobs:
if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Check file sizes
@@ -241,7 +239,7 @@ jobs:
cat file_size_report.txt
exit 1
fi
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'File size report'
@@ -269,26 +267,26 @@ jobs:
ports:
- 5432:5432
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Cache .planemo
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-planemo
with:
path: ~/.planemo
key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
- uses: SimenB/github-actions-cpu-cores@v1
+ uses: SimenB/github-actions-cpu-cores@v2
id: cpu-cores
- name: Clean dotnet folder for space
run: rm -Rf /usr/share/dotnet
@@ -319,7 +317,7 @@ jobs:
galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
# Limit each test to 15 minutes
test_timeout: 1800
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
@@ -338,14 +336,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- - uses: actions/download-artifact@v3
+ - uses: actions/download-artifact@v4
with:
path: artifacts
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -357,7 +355,7 @@ jobs:
mode: combine
html-report: true
markdown-report: true
- - uses: actions/upload-artifact@v3
+ - uses: actions/upload-artifact@v4
with:
name: 'All tool test results'
path: upload
@@ -384,14 +382,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
fetch-depth: 1
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
- uses: actions/cache@v3
+ uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
@@ -425,7 +423,7 @@ jobs:
with:
sha: ${{ github.event.after }}
- name: Create comment
- uses: peter-evans/create-or-update-comment@v2
+ uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
issue-number: ${{ steps.getpr.outputs.number }}
diff --git a/tools/sleepwaste/.shed.yml b/tools/sleepwaste/.shed.yml
new file mode 100644
index 00000000..a389de88
--- /dev/null
+++ b/tools/sleepwaste/.shed.yml
@@ -0,0 +1,10 @@
+name: sleepwaste
+owner: mbernt
+description: sleepwaste
+long_description: |
+ Waste time and memory
+categories:
+- Text Manipulation
+homepage_url: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/sleepwaste
+remote_repository_url: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/sleepwaster/
+type: unrestricted
\ No newline at end of file
diff --git a/tools/sleepwaste/sleepwaste-c b/tools/sleepwaste/sleepwaste-c
new file mode 100755
index 00000000..7d94c7e5
Binary files /dev/null and b/tools/sleepwaste/sleepwaste-c differ
diff --git a/tools/sleepwaste/sleepwaste-cpp b/tools/sleepwaste/sleepwaste-cpp
new file mode 100755
index 00000000..8a16bfac
Binary files /dev/null and b/tools/sleepwaste/sleepwaste-cpp differ
diff --git a/tools/sleepwaste/sleepwaste.py b/tools/sleepwaste/sleepwaste.py
index 4925a462..01b09894 100644
--- a/tools/sleepwaste/sleepwaste.py
+++ b/tools/sleepwaste/sleepwaste.py
@@ -10,4 +10,4 @@
array = " "*(args.memory*1024*1024)
time.sleep( args.time )
-print "slept for {time} s and {memory} MB".format( time = args.time, memory = args.memory )
+print("slept for {time} s and {memory} MB".format( time = args.time, memory = args.memory ))
diff --git a/tools/sleepwaste/sleepwaste.xml b/tools/sleepwaste/sleepwaste.xml
index 6635d644..7dbfbc7c 100644
--- a/tools/sleepwaste/sleepwaste.xml
+++ b/tools/sleepwaste/sleepwaste.xml
@@ -5,23 +5,23 @@
'$ofile'
- ]]>
+ #elif $language == "python":
+ python $__tool_directory__/sleepwaste.py
+ #elif $language == "cpp":
+ $__tool_directory__/sleepwaste-cpp
+ #elif $language == "c":
+ $__tool_directory__/sleepwaste-c
+ #elif $language == "perl":
+ perl $__tool_directory__/sleepwaste.pl
+ #elif $language == "java":
+ java -classpath $__tool_directory__ -Xmx4548m sleepwaste
+ #end if
+ '$time' '$memory' > '$ofile'
+ ]]>
@@ -33,70 +33,69 @@
-
-
+
-
+
+
+
+
+
+
+
-
-
+
+
+
-
-
+
+
-
-
+
+
+
-
-
+
+
+
-
+
-
-
+
+
+
-
+
-
-
-
-
+
+
+
+